Single molecule studies of ligand-DNA interactions using atomic force microscopy

This thesis describes the results of experiments into the intra and inter-molecular binding of various ligands with dsDNA via the mechanism of intercalation, principally using the technique of atomic force microscopy (AFM). Since the description of the first AFM in the mid 1980’s, AFM has emerged as a sensitive and versatile analytical tool, capable both of detecting and manipulating artefacts at picometer resolutions. In these studies, AFM imaging, supported by circular dichroism, reveals unusual conformational changes in DNA that occur as a result of the binding of ligands that incorporate the acridine chromophore. These changes are distinct from those observed following the binding of other intercalators such as doxorubicin and echinomycin. Direct measurement of the length of linear DNA strands bound to acridine based ligands reveals a shortening of the DNA at very low ligand concentrations. This observation suggests that the structural changes that occur in DNA following the intercalation of the acridine chromophore are more wide ranging than previously thought and support molecular modeling studies that have proposed that the intercalated DNA duplex exhibits characteristics of both B and A form DNA. Variations in the conformational changes that occur in DNA as a result of intercalation may have implications for the application of new intercalating ligands as chemotherapeutic agents. In addition, single molecule force spectroscopy has been used to examine the capacity of bisintercalators to bind to DNA in an inter-molecular fashion. By stretching individual strands of dsDNA, acridine dimers are shown to bind to separate strands of DNA. Intermolecular binding of this kind remains an unexplored cytotoxic mechanism that may yet find an application in vivo. This observation is supported by a novel assay that utilises the controlled aggregation of gold nanoparticles. These nanoparticles, functionalised with DNA, are shown to aggregate on addition of a bisintercalator. The aggregation is fully reversible with the addition of sodium dodecylsulphate. These force spectroscopy experiments have also uncovered a previously unobserved, intermolecular binding mode of the peptide antibiotics echinomycin and TANDEM. In certain circumstances, these ligands are revealed to bind exclusively to the termini of separate DNA strands in a sequence dependent fashion. This finding may have implications for the employment of these ligands in the nanosciences, as a tool for joining short pieces of DNA or improving the efficiency of the enzymatic, blunt-end ligation of DNA

The Transit Light Source Effect: False Spectral Features and Incorrect Densities for M-dwarf Transiting Planets

Transmission spectra are differential measurements that utilize stellar illumination to probe transiting exoplanet atmospheres. Any spectral difference between the illuminating light source and the disk-integrated stellar spectrum due to starspots and faculae will be imprinted in the observed transmission spectrum. However, few constraints exist for the extent of photospheric heterogeneities in M dwarfs. Here, we model spot and faculae covering fractions consistent with observed photometric variabilities for M dwarfs and the associated 0.3-5.5 $\mu$m stellar contamination spectra. We find that large ranges of spot and faculae covering fractions are consistent with observations and corrections assuming a linear relation between variability amplitude and covering fractions generally underestimate the stellar contamination. Using realistic estimates for spot and faculae covering fractions, we find stellar contamination can be more than $10 \times$ larger than transit depth changes expected for atmospheric features in rocky exoplanets. We also find that stellar spectral contamination can lead to systematic errors in radius and therefore the derived density of small planets. In the case of the TRAPPIST-1 system, we show that TRAPPIST-1's rotational variability is consistent with spot covering fractions $f_{spot} = 8^{+18}_{-7}\%$ and faculae covering fractions $f_{fac} = 54^{+16}_{-46}\%$. The associated stellar contamination signals alter transit depths of the TRAPPIST-1 planets at wavelengths of interest for planetary atmospheric species by roughly 1-15 $\times$ the strength of planetary features, significantly complicating $JWST$ follow-up observations of this system. Similarly, we find stellar contamination can lead to underestimates of bulk densities of the TRAPPIST-1 planets of $\Delta(\rho) = -3^{+3}_{-8} \%$, thus leading to overestimates of their volatile contents.Comment: accepted for publication in Ap

Towards robust corrections for stellar contamination in JWST exoplanet transmission spectra

Transmission spectroscopy is still the preferred characterization technique for exoplanet atmospheres, although it presents unique challenges which translate into characterization bottlenecks when robust mitigation strategies are missing. Stellar contamination is one of such challenges that can overpower the planetary signal by up to an order of magnitude, and thus not accounting for stellar contamination can lead to significant biases in the derived atmospheric properties. Yet, accounting for stellar contamination may not be straightforward, as important discrepancies exist between state-of-the-art stellar models and measured spectra and between models themselves. Here we explore the extent to which stellar models can be used to reliably correct for stellar contamination and yield a planet's uncontaminated transmission spectrum. We find that (1) discrepancies between stellar models can dominate the noise budget of JWST transmission spectra of planets around stars with heterogeneous photospheres; (2) the true number of unique photospheric spectral components and their properties can only be accurately retrieved when the stellar models have a sufficient fidelity; and (3) under such optimistic circumstances the contribution of stellar contamination to the noise budget of a transmission spectrum is considerably below that of the photon noise for the standard transit observation setup. Therefore, we suggest (1) increased efforts towards development of model spectra of stars and their active regions in a data-driven manner; and (2) the development of empirical approaches for deriving spectra of photospheric components using the observatories with which the atmospheric explorations are carried out.Comment: 15 pages, 8 figures, 2 table

Empirically Constraining the Spectra of a Stars Heterogeneities From Its Rotation Lightcurve

Transmission spectroscopy is currently the most powerful technique to study a wide range of planetary atmospheres, leveraging the filtering of a stars light by a planets atmosphere rather than its own emission. However, both a planet and its star contribute to the information encoded in a transmission spectrum and a particular challenge relate to disentangling their contributions. As measurements improve, the lack of fidelity of stellar spectra models present a bottleneck for accurate disentanglement. Considering JWST and future high-precision spectroscopy missions, we investigate the ability to derive empirical constraints on the emission spectra of stellar surface heterogeneities (i.e., spots and faculae) using the same facility as used to acquire the transmission spectra intended to characterize a given atmosphere. Using TRAPPIST-1 as a test case, we demonstrate that it is possible to constrain the photospheric spectrum to 0.2% and the spectra of stellar heterogeneities to within 1-5%, which will be valuable benchmarks to inform the new generation of theoretical stellar models. Long baseline of observations (90% of the stellar rotation period) are necessary to ensure the photon-limited (i.e., instrument-limited) exploration of exoplanetary atmospheres via transmission spectroscopy.Comment: 10 pages, 3 figure

The Near-Infrared Transmission Spectra of TRAPPIST-1 Planets b, c, d, e, f, and g and Stellar Contamination in Multi-Epoch Transit Spectra

The seven approximately Earth-sized transiting planets in the \object{TRAPPIST-1} system provide a unique opportunity to explore habitable zone and non-habitable zone small planets within the same system. Its habitable zone exoplanets -- due to their favorable transit depths -- are also worlds for which atmospheric transmission spectroscopy is within reach with the Hubble Space Telescope (HST) and with the James Webb Space Telescope (JWST). We present here an independent reduction and analysis of two \textit{HST} Wide Field Camera 3 (WFC3) near-infrared transit spectroscopy datasets for six planets (b through g). Utilizing our physically-motivated detector charge trap correction and a custom cosmic ray correction routine, we confirm the general shape of the transmission spectra presented by \textbf{\citet{deWit2016, deWit2018}}. Our data reduction approach leads to a 25\% increase in the usable data and reduces the risk of confusing astrophysical brightness variations (e.g., flares) with instrumental systematics. No prominent absorption features are detected in any individual planet's transmission spectra; by contrast, the combined spectrum of the planets shows a suggestive decrease around 1.4\,\micron similar to an inverted water absorption feature. Including transit depths from \textit{K2}, the SPECULOOS-South Observatory, and \textit{Spitzer}, we find that the complete transmission spectrum is fully consistent with stellar contamination owing to the transit light source effect. These spectra demonstrate how stellar contamination can overwhelm planetary absorption features in low-resolution exoplanet transit spectra obtained by \textit{HST} and \textit{JWST} and also highlight the challenges in combining multi epoch observations for planets around rapidly rotating spotted stars.Comment: 41 pages, 20 figures. Accepted for publication on AJ on 8/28/2018. Comments and suggestions are welcom

Can 1D radiative equilibrium models of faculae be used for calculating contamination of transmission spectra?

The reliable characterization of planetary atmospheres with transmission spectroscopy requires realistic modeling of stellar magnetic features, since features that are attributable to an exoplanet atmosphere could instead stem from the host star's magnetic activity. Current retrieval algorithms for analysing transmission spectra rely on intensity contrasts of magnetic features from 1D radiative-convective models. However, magnetic features, especially faculae, are not fully captured by such simplified models. Here we investigate how well such 1D models can reproduce 3D facular contrasts, taking a G2V star as an example. We employ the well established radiative magnetohydrodynamic code MURaM to obtain three-dimensional simulations of the magneto-convection and photosphere harboring a local small-scale-dynamo. Simulations without additional vertical magnetic fields are taken to describe the quiet solar regions, while simulations with initially 100 G, 200 G and 300 G vertical magnetic fields are used to represent different magnetic activity levels. Subsequently, the spectra emergent from the MURaM cubes are calculated with the MPS-ATLAS radiative transfer code. We find that the wavelength dependence of facular contrast from 1D radiative-convective models cannot reproduce facular contrasts obtained from 3D modeling. This has far reaching consequences for exoplanet characterization using transmission spectroscopy, where accurate knowledge of the host star is essential for unbiased inferences of the planetary atmospheric properties.Comment: 7 pages, 2 figures, submitted to APJ